Functional decomposition is an important and powerful technique in the logic synthesis. The ternary matrix cover approach is one of the existing methods of this type. This method is also used in decomposition of a system of completely specified Boolean functions. Before constructing the desired superposition, it needs to encode a table. There is a trivial encoding method. But to find a better solution, it is important to use a special approach, because the result of the encoding has a direct influence on the obtained functions. In this paper, an efficient algorithm to encode this table is presented. It uses the approach connected with the assembling Boolean hyper cube method. The proposed algorithm is explained in details with an example. The benefits and impacts of the suggested technique are also discussed.